Expression profiling of the cerebral ischemic and hypoxic response

In mammals, the major component in energy production is molecular oxygen. This has led to the development of several elaborate strategies that tightly regulate oxygen homeostasis in order to allow appropriate cell function and survival. However, a sustained drop in oxygen supply to neuronal tissue has detrimental consequences to cell functioning and survival. Disturbances in oxygen supply have been implicated in a number of CNS disorders that can be related to hypoxia or ischemia. On a cellular level, oxygen-deprived stress induces a multitude of spatially and temporally regulated responses, ranging from adapted channel activity to altered gene expression. Global analysis of expression changes over several time points and tissue regions or cells has already shed light on previous known and unknown biological processes and molecules. By combining knowledge from several different expression-profiling studies into one database, the first steps are made in unifying and categorizing the molecular response to oxygen-deprived conditions, such as stroke. In this review, some of the queries that can be extracted from the database are discussed in regard to the biological context.     

Response of Chinese hamster v79 multicellular spheroids exposed to high-energy carbon ions

Chinese hamster V79-379A spheroids 200 +/- 30 microm (+/- SD) in diameter were irradiated in agitated medium in different oxygen atmospheres with (1) 227 MeV/nucleon (12)C(+6) ions (plateau region) to model tissue in the entrance channel during therapy, (2) carbon ions in the extended Bragg peak modeling tissue in the target volume, or (3) X rays as a reference modality. Cell survival curves were similar for modes (1) and (3), indicating the absence of a contact effect and the presence of a pronounced oxygen effect with oxygen enhancement ratios (OERs) of 2.8 and 2.9, respectively. In contrast, the oxygen effect was substantially smaller in mode (2) with an OER of 1.4. Under normal or restricted oxygen supply conditions (external pO(2) = 145 or 0 mmHg), the relative biological effectiveness (RBE) was 2.1 or 4.3, respectively, for Bragg-peak irradiation. This modality induced apoptosis and a dose-dependent accumulation of cells in G(2)/M phase even at pO(2) = 0 mmHg. The volume ratios of treated to untreated spheroids exhibited cyclic variations after heavy-particle treatment that were not directly attributable to cell cycle synchronization. In summary, the results suggest that carbon ions in the extended Bragg peak are more effective than conventional X rays, particularly under hypoxic conditions.     

Modeling spatial distribution of oxygen in 3d culture of islet beta‐cells

Three‐dimensional (3D) scaffold culture of pancreatic β‐cell has been proven to be able to better mimic physiological conditions in the body. However, one critical issue with culturing pancreatic β‐cells is that β‐cells consume large amounts of oxygen, and hence insufficient oxygen supply in the culture leads to loss of β‐cell mass and functions. This becomes more significant when cells are cultured in a 3D scaffold. In this study, in order to understand the effect of oxygen tension inside a cell‐laden collagen culture on β‐cell proliferation, a culture model with encapsulation of an oxygen‐generator was established. The oxygen‐generator was made by embedding hydrogen peroxide into nontoxic polydimethylsiloxane to avoid the toxicity of a chemical reaction in the β‐cell culture. To examine the effectiveness of the oxygenation enabled 3D culture, the spatial‐temporal distribution of oxygen tension inside a scaffold was evaluated by a mathematical modeling approach. Our simulation results indicated that an oxygenation‐aided 3D culture would augment the oxygen supply required for the β‐cells. Furthermore, we identified that cell seeding density and the capacity of the oxygenator are two critical parameters in the optimization of the culture. Notably, cell‐laden scaffold cultures with an in situ oxygen supply significantly improved the β‐cells' biological function. These β‐cells possess high insulin secretion capacity. The results obtained in this work would provide valuable information for optimizing and encouraging functional β‐cell cultures. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:221–228, 2017     

A mathematical model of electron transfer within the mitochondrial respiratory cytochromes

A simple mathematical model of electron flow along the mitochondrial respiratory cytochrome assembly and the transfer of electrons to molecular oxygen is presented. First, an expression for the current-voltage relationship for a biological oxygen electrode is derived, and from this the relationship between oxygen consumption rate and oxygen partial pressure is determined. An independent relationship between mitochondrial oxygen partial pressure and oxygen supply rate is then derived. By eliminating oxygen partial pressure from these two expressions, we may obtain a relationship between oxygen supply rate and oxygen consumption rate. This model is then used to investigate the effects of tissue dysoxia, uncoupling of oxidative phosphorylation, increased cellular diffusional resistance and inhomogeneities in oxygen supply on oxygen consumption. It is concluded that each of the above contribute in varying degrees to the phenomenon of "pathological oxygen supply dependency".     

The role of calcium in hypoxia-induced signal transduction and gene expression

Mammalian cells require a constant supply of oxygen in order to maintain adequate energy production, which is essential for maintaining normal function and for ensuring cell survival. Sustained hypoxia can result in cell death. Sophisticated mechanisms have therefore evolved which allow cells to respond and adapt to hypoxia. Specialized oxygen-sensing cells have the ability to detect changes in oxygen tension and transduce this signal into organ system functions that enhance the delivery of oxygen to tissue in a wide variety of different organisms. An increase in intracellular calcium levels is a primary response of many cell types to hypoxia/ischemia. The response to hypoxia is complex and involves the regulation of multiple signaling pathways and coordinated expression of perhaps hundreds of genes. This review discusses the role of calcium in hypoxia-induced regulation of signal transduction pathways and gene expression. An understanding of the molecular events initiated by changes in intracellular calcium will lead to the development of therapeutic approaches toward the treatment of hypoxic/ischemic diseases and tumors.     

Cellular and transcriptomic analysis of NS0 cell response during exposure to hypoxia

Mammalian cells have the ability to alter their gene expression in order to survive or adapt to a variety of environment stresses including hypoxic stress. Maintaining oxygen supply has been accepted as essential for cell survival and growth. To determine the cellular and molecular changes which take place under oxygen deprivation, an NS0 cell line producing a human-mouse chimeric antibody was cultured under hypoxic conditions (<1%). Various cellular parameters such as viability, productivity, metabolism, apoptosis and cell cycle were studied and notable changes were shown to be accompanied by changes in metabolic rates. When the cells where exposed to hypoxia for 48 h, cell growth was suppressed and cell death was detected. To better understand and explore the mechanisms underpinning these biological alterations and to identify the genes involved in the genetic reprogramming, genome-wide analyses were performed using GeneChip Mouse Genome arrays. The gene expression profiling generated by the microarray technique revealed that hypoxia, even in the early stages (12h), induces significant changes in gene expression in NS0 cells. The primary responses to hypoxia within the cells were: (1) the up-regulation of pathways such as glycolysis that ultimately lead to alternative routes of ATP generation and increased oxygen availability; and (2) the down-regulation of genes involved in purine/pyrimidine and one carbon pool metabolisms required for DNA and RNA synthesis. By combining gene expression and physiological changes under hypoxia, it was possible to explore the mechanisms of hypoxia-induced alterations in more depth.     

Hydroxytyrosol prevents dermal papilla cells inflammation under oxidative stress by inducing autophagy

Hydroxytyrosol (HT), a primary phenolic antioxidant in olive oil, can afford protection from oxidative stress (OS) in different cells, including skin cells. In particular, it regulates several inflammation‐associated processes as well as in improving the antioxidant defense system. However, there is no information about HT used in the treatment of hair loss. This work aimed at exploring the potential protective actions of HT against OS in rat dermal papilla cells. After treatment, the related expression of protein and messenger RNA were detected using morphological and molecular analyses. The results showed that HT significantly reduced intracellular reactive oxygen species level, apoptotic markers and inflammation induced by OS and enhanced cell survival by regulating autophagy. Furthermore, HT enhanced the secretion of hair growth factors in the anti‐inflammation process. These results suggest that HT has a significant protective ability against OS and encourage the use of this biological ingredient as a possible tool to prevent alopecia.     

HOXD-AS1 is a predictor of clinical progression and functions as an oncogenic lncRNAs in papillary thyroid cancer

Long noncoding RNA HOXD cluster antisense RNA 1 (HOXD-AS1) has been found to play a crucial role in the tumorigenesis and progression of human cancer. However, the role of HOXD-AS1 in papillary thyroid cancer is still unknown. The purpose of this study was to investigate the clinical value and biological function of HOXD-AS1 in papillary thyroid cancer. The results showed HOXD-AS1 is overexpressed in papillary thyroid cancer tissues and cell lines compared with matching nontumor tissue specimens and normal thyroid cell line, respectively. High expression of HOXD-AS1 was associated with elderly people, advanced clinical stage, large tumor size, present lymph node metastasis, and distant metastasis. There was no significant correlation between HOXD-AS1 expression and disease-free survival or overall survival in this cohort from the TCGA database. The study in vitro suggested reduced HOXD-AS1 expression inhibited papillary thyroid cancer cell proliferation, migration, and invasion, and promoted cell-cycle arrest. In conclusion, HOXD-AS1 is a biomarker for predicting clinical progression in papillary thyroid cancer.     

Persistence of CD34 Stem Marker in Human Lipoma: Searching for Cancer Stem Cells

Background: Lipomas are benign solid tumours that develop in soft tissues with origin in mesenchymal progenitors. Macroscopically, they appear as soft-elastic nodules, varying in volume from a few millimiters to several centimetres and can enlarge progressively. Although they are usually asymptomatic, they can cause symptoms due to nerve or vessel compression. Microscopically they appear as fibrous connective tissue stroma with embedded adipocytes, and absence of inflammation. Up to now no characterisation of stem cell population present in this tissue has been performed.Methods: Cytofluorimetric, biological and molecular biology analyses have been performed in order to test superficial cell markers and gene expression profile related to stemness and apoptotic activity of cells present in lipoma tissues compared to those of adipose tissue''s cells.Results: Our results confirmed that CD34⁺ cells in lipoma were present around small adipocytes, showing several altered biological activity such as proliferation, apoptotis and stemness.Conclusions: The data emerging from the comparison of the lipoma cells and normal adipose tissue, suggests the presence of cell precursors involved in the development of the lipoma. This hypothesis requires further investigation and may indicate new thresholds in the study of benign tumour pathogenesis.     

Anoxia or oxygen and glucose deprivation in SH-SY5Y cells: a step closer to the unraveling of neuroglobin and cytoglobin functions

Several studies support the hypothesis that neuroglobin and cytoglobin play a protective role against cell death when cellular oxygen supply is critical. Although the underlying molecular mechanisms are unknown, previous reports suggest that this protection can be realised by the fact that they act as ROS scavengers. In this study, expression of neuroglobin and cytoglobin was evaluated in a human neuroblastoma cell line (SH-SY5Y) under conditions of anoxia or oxygen and glucose deprivation (OGD). The cells could survive prolonged anoxia without significant loss of viability. They became anoxia sensitive when deprived of glucose. OGD induced significant cell death after 16 h resulting in 54% dead cells after 32 h. Necrosis was the main process involved in OGD-induced cell death. After reoxygenation, apoptotic neurons became more abundant. Real-time quantitative PCR and Western blotting revealed that neuroglobin and cytoglobin were upregulated, the former under OGD and the latter under anoxic conditions. Under OGD, cell survival was significantly reduced after inhibiting cytoglobin expression by transfection with antisense ODN. Moreover, cell survival was significantly enhanced by neuroglobin or cytoglobin overexpression. When neuroglobin or cytoglobin protein expression increased or decreased, the H(2)O(2) level was found to be lower or higher, respectively. We conclude that neuroglobin or cytoglobin act as ROS scavengers under ischemic conditions.     

HIFs and tumors--causes and consequences

For most organisms oxygen is essential fo life. When oxygen levels drop below those required to maintain the minimum physiological oxygen requirement of an organism or tissue it is termed hypoxia. To counter act possible deleterious effects of such a state, an immediate molecular response is initiated causing adaptation responses aimed at cell survival. This response is mediated by the hypoxia-inducible factor-1 (HIF-1), which is a heterodimer consisting of an alpha- and a beta-subunit. HIF-1 alpha protein is stabilized under hypoxic conditions and therefore confers selectivity to this response. Hypoxia is characteristic of tumors, mainly because of impaired blood supply resulting from abnormal growth. Over the past few years enormous progress has been made in the attempt to understand how the activation of the physiological response to hypoxia influences neoplastic growth. In this review some aspects of HIF-1 pathway activation in tumors and the consequences for pathophysiology and treatment of neoplasia are discussed.     

Methionine sulfoxide reductase A: Structure, function and role in ocular pathology

Methionine is a highly susceptible amino acid that can be oxidized to S and R diastereomeric forms of methionine sulfoxide by many of the reactive oxygen species generated in biological systems. Methionine sulfoxide reductases (Msrs) are thioredoxin-linked enzymes involved in the enzymatic conversion of methionine sulfoxide to methionine. Although MsrA and MsrB have the same function of methionine reduction, they differ in substrate specifi city, active site composition, subcellular localization, and evolution. MsrA has been localized in different ocular regions and is abundantly expressed in the retina and in retinal pigment epithelial (RPE) cells. MsrA protects cells from oxidative stress. Overexpression of MsrA increases resistance to cell death, while silencing or knocking down MsrA decreases cell survival; events that are mediated by mitochondria. MsrA participates in protein-protein interaction with several other cellular proteins. The interaction of MsrAwith α-crystallins is of utmost importance given the known functions of the latter in protein folding, neuroprotection, and cell survival. Oxidation of methionine residues in α-crystallins results in loss of chaperone function and possibly its antiapoptotic properties. Recent work from our laboratory has shown that MsrA is co-localized with αA and αB crystallins in the retinal samples of patients with age-related macular degen- eration. We have also found that chemically induced hypoxia regulates the expression of MsrA and MsrB2 in human RPE cells. Thus, MsrA is a critical enzyme that participates in cell and tissue protection, and its interaction with other proteins/growth factors may provide a target for therapeutic strategies to prevent degenerative diseases.     

Characterization of tissue scaffolds for time-dependent biotransport criteria – a novel computational procedure

This study aims to establish a new computational framework that allows modeling transient oxygen diffusion in tissue scaffolds more efficiently. It has been well known that the survival of cells strongly relies on continuous oxygen/nutrient supply and metabolite removal. With optimal design in scaffold architecture, its ability to sustain long distance oxygen supply could be improved considerably. In this study, finite element based homogenization procedure is first used to characterize the initial effective biotransport properties in silico. These initial properties are proper indicators to prediction of the on-going performance of tissue scaffolds over time. The transient model by adopting an edge-based smoothed finite element method with combination of mass-redistributed method is then established to more efficiently simulate the transient oxygen transfer process in tissue scaffolds. The proposed new method allows large time steps to model the oxygen diffusion process without losing numerical accuracy, thereby enhancing the computational efficiency significantly, in particular for the design optimization problems which typically require numerous analysis iterations. A number of different scaffold designs are examined either under net diffusion without cell seeding, or under cellular oxygen/nutrient uptake with or without considering cell viability. The association between the homogenized effective diffusivity of net scaffold microstructures and corresponding transient diffusion and time-dependent cellular activities is divulged. This study provides some insights into scaffold design.     

Chemical and molecular mechanisms of antioxidants: experimental approaches and model systems

Free radicals derived from oxygen, nitrogen and sulphur molecules in the biological system are highly active to react with other molecules due to their unpaired electrons. These radicals are important part of groups of molecules called reactive oxygen/nitrogen species (ROS/RNS), which are produced during cellular metabolism and functional activities and have important roles in cell signalling, apoptosis, gene expression and ion transportation. However, excessive ROS attack bases in nucleic acids, amino acid side chains in proteins and double bonds in unsaturated fatty acids, and cause oxidative stress, which can damage DNA, RNA, proteins and lipids resulting in an increased risk for cardiovascular disease, cancer, autism and other diseases. Intracellular antioxidant enzymes and intake of dietary antioxidants may help to maintain an adequate antioxidant status in the body. In the past decades, new molecular techniques, cell cultures and animal models have been established to study the effects and mechanisms of antioxidants on ROS. The chemical and molecular approaches have been used to study the mechanism and kinetics of antioxidants and to identify new potent antioxidants. Antioxidants can decrease the oxidative damage directly via reacting with free radicals or indirectly by inhibiting the activity or expression of free radical generating enzymes or enhancing the activity or expression of intracellular antioxidant enzymes. The new chemical and cell-free biological system has been applied in dissecting the molecular action of antioxidants. This review focuses on the research approaches that have been used to study oxidative stress and antioxidants in lipid peroxidation, DNA damage, protein modification as well as enzyme activity, with emphasis on the chemical and cell-free biological system.     

A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells

The advent of functional genomics has enabled the genome-wide characterization of the molecular state of cells and tissues, virtually at every level of biological organization. The difficulty in organizing and mining this unprecedented amount of information has stimulated the development of computational methods designed to infer the underlying structure of regulatory networks from observational data. These important developments had a profound impact in biological sciences since they triggered the development of a novel data-driven investigative approach. In cancer research, this strategy has been particularly successful. It has contributed to the identification of novel biomarkers, to a better characterization of disease heterogeneity and to a more in depth understanding of cancer pathophysiology. However, so far these approaches have not explicitly addressed the challenge of identifying networks representing the interaction of different cell types in a complex tissue. Since these interactions represent an essential part of the biology of both diseased and healthy tissues, it is of paramount importance that this challenge is addressed. Here we report the definition of a network reverse engineering strategy designed to infer directional signals linking adjacent cell types within a complex tissue. The application of this inference strategy to prostate cancer genome-wide expression profiling data validated the approach and revealed that normal epithelial cells exert an anti-tumour activity on prostate carcinoma cells. Moreover, by using a Bayesian hierarchical model integrating genetics and gene expression data and combining this with survival analysis, we show that the expression of putative cell communication genes related to focal adhesion and secretion is affected by epistatic gene copy number variation and it is predictive of patient survival. Ultimately, this study represents a generalizable approach to the challenge of deciphering cell communication networks in a wide spectrum of biological systems.     

The Guanine Nucleotide Exchange Factor SWAP-70 Modulates the Migration and Invasiveness of Human Malignant Glioma Cells

The malignant glioma is the most common primary human brain tumor. Its tendency to invade away from the primary tumor mass is considered a leading cause of tumor recurrence and treatment failure. Accordingly, the molecular pathogenesis of glioma invasion is currently under investigation. Previously, we examined a gene expression array database comparing human gliomas to nonneoplastic controls and identified several Rac guanine nucleotide exchange factors with differential expression. Here, we report that the guanine nucleotide exchange factor SWAP-70 has increased expression in malignant gliomas and strongly correlates with lowered patient survival. SWAP-70 is a multifunctional signaling protein involved in membrane ruffling that works cooperatively with activated Rac. Using a glioma tissue microarray, we validated that SWAP-70 demonstrates higher expression in malignant gliomas compared with low-grade gliomas or nonneoplastic brain tissue. Through immunofluorescence, SWAP-70 localizes to membrane ruffles in response to the growth factor, epidermal growth factor. To assess the role of SWAP-70 in glioma migration and invasion, we inhibited its expression withsmall interfering RNAs and observed decreased glioma cell migration and invasion. SWAP-70 overexpression led to increased levels of active Rac even in low-serum conditions. In addition, when SWAP-70 was overexpressed in glioma cells, we observed enhanced membrane ruffle formation followed by increased cellmigration and invasiveness. Taken together, our findings suggest that the guanine nucleotide exchange factor SWAP-70 plays an important role in the migration and invasion of human gliomas into the surrounding tissue.     

Why is the partial oxygen pressure of human tissues a crucial parameter? Small molecules and hypoxia

Oxygen supply and diffusion into tissues are necessary for survival. The oxygen partial pressure (pO(2)), which is a key component of the physiological state of an organ, results from the balance between oxygen delivery and its consumption. In mammals, oxygen is transported by red blood cells circulating in a well-organized vasculature. Oxygen delivery is dependent on the metabolic requirements and functional status of each organ. Consequently, in a physiological condition, organ and tissue are characterized by their own unique 'tissue normoxia' or 'physioxia' status. Tissue oxygenation is severely disturbed during pathological conditions such as cancer, diabetes, coronary heart disease, stroke, etc., which are associated with decrease in pO(2), i.e. 'hypoxia'. In this review, we present an array of methods currently used for assessing tissue oxygenation. We show that hypoxia is marked during tumour development and has strong consequences for oxygenation and its influence upon chemotherapy efficiency. Then we compare this to physiological pO(2) values of human organs. Finally we evaluate consequences of physioxia on cell activity and its molecular modulations. More importantly we emphasize the discrepancy between in vivo and in vitro tissue and cells oxygen status which can have detrimental effects on experimental outcome. It appears that the values corresponding to the physioxia are ranging between 11% and 1% O(2) whereas current in vitro experimentations are usually performed in 19.95% O(2), an artificial context as far as oxygen balance is concerned. It is important to realize that most of the experiments performed in so-called normoxia might be dangerously misleading.